Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(biomaRt)
library(fgsea)
library(goseq)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "Micro-PVM"
graph_weight
## [1] "10.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   38.00   40.00   41.00   41.38   43.00   44.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 38 39 39 39 39 39 40 40 40 40 40 40 40 40 41 41 41 41 41 41 41 42 42 42 42
## [26] 42 43 43 43 43 43 43 43 43 43 43 43 44 44 44

Find gene symbols

Find gene symbols from bioMart.

All the gene symbols that can be found in bioMart are consistent with what we have. So no need to run it.

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"), 
                filters = "external_gene_name", 
                values = assayed_genes, 
                mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]

table(assayed_genes %in% gene_BM$external_gene_name)

t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]

table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}

table(is.na(a2s))
## 
## FALSE  TRUE 
##  1739   261
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    21  1718   261
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##     sym_in_data   sym_limma
##  1:       LRRC6     DNAAF11
##  2:    C11orf49      CSTPP1
##  3:   LINC00476 ERCC6L2-AS1
##  4:  HNRNPA1P48   HNRNPA1L3
##  5:  ZRANB2-AS2   ZRANB2-DT
##  6:   LINC00271     AHI1-DT
##  7:    RFX3-AS1     RFX3-DT
##  8:   LINC00884  ATP13A3-DT
##  9:   FBXO30-DT    EPM2A-DT
## 10:   LINC00894    EOLA2-DT
## 11:   COX10-AS1    COX10-DT
## 12:   LINC01184  SLC12A2-DT
## 13: FAM198B-AS1  GASK1B-AS1
## 14:     C5orf17   LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16:   LINC01146       HISLA
## 17:      BTBD11       ABTB3
## 18:       H2BU1      H2BC26
## 19:      SKIV2L       SKIC2
## 20:     FAM155A       NALF1
## 21:  CTB-41I6.2   PIK3R5-DT
##     sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 2000    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
## 3:        PDK4      PDK4        PDK4
## 4:       CALCR     CALCR       CALCR
## 5:       ABCB4     ABCB4       ABCB4
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1 
## 2000

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"
sapply(pathways, length)
## reactome    go_bp 
##     1692     7647

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

Conduct enrichment analysis

dim(gene_info)
## [1] 2000    3
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
gene_dat = fread(sprintf("data/%s_genes_info.csv", cell_type_name))
dim(gene_dat)
## [1] 36517     9
gene_dat[1:2,]
##           gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003               FALSE       TSPAN6    NCBITaxon:9606
## 2: ENSG00000000005               FALSE         TNMD    NCBITaxon:9606
##    feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1:            gene                76    0.002350               99.8100
## 2:            gene                 1    0.000025               99.9975
##    total_counts
## 1:           94
## 2:            1
length(unique(gene_info$sym_in_data))
## [1] 2000
table(gene_info$sym_in_data %in% gene_dat$feature_name)
## 
## TRUE 
## 2000
table(gene_dat$feature_name %in% gene_info$sym_in_data)
## 
## FALSE  TRUE 
## 34517  2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1

table(gene_dat$selected)
## 
##     0     1 
## 34517  2000
tapply(gene_dat$pct_dropout_by_counts, gene_dat$selected, summary)
## $`0`
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    0.00   94.48   99.58   93.53   99.97  100.00 
## 
## $`1`
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6475 65.5944 84.3650 76.3053 93.6756 97.9950
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data", 
                  by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)
## [1] 2000   12
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol        gene_ids feature_is_filtered
## 1:        AATK      AATK        AATK ENSG00000181409               FALSE
## 2:        ABAT      ABAT        ABAT ENSG00000183044               FALSE
##    feature_reference feature_biotype n_cells_by_counts mean_counts
## 1:    NCBITaxon:9606            gene              3157    0.091525
## 2:    NCBITaxon:9606            gene              9074    0.368950
##    pct_dropout_by_counts total_counts selected
## 1:               92.1075         3661        1
## 2:               77.3150        14758        1
max_n2kp = 10

goseq_res = NULL

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info$sym_in_data %in% gene_sets[[k]]
  names(genes) = gene_info$gene_symbol
  table(genes)
  
  pwf = nullp(genes, "hg38", "geneSymbol", 
              bias.data = 100 - gene_info$pct_dropout_by_counts)
  
  for(k1 in names(pathways)){
    p1 = pathways[[k1]]
    res1 = goseq(pwf, "hg38", "geneSymbol", 
                 gene2cat=goseq:::reversemapping(p1))
    res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
    
    nD = sum(res1$FDR < 0.05)
    
    if(nD > 0){
      res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
      res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
      res1$category = gsub("_", " ", res1$category)
      res1$category = tolower(res1$category)
      res1$category = substr(res1$category, start=1, stop=81)
      goseq_res[[set_k]][[k1]] = res1
    }
  }
}
## [1] 1
##  [1] "SIGLEC1"      "CRYM"         "RIPOR2"       "GLT1D1"       "ADGRA3"      
##  [6] "PID1"         "ADAMTS3"      "PAPSS2"       "GOLGA8B"      "HDAC4-AS1"   
## [11] "MEIKIN"       "RP11-120A1.1" "TRG-AS1"      "IGSF9B"       "LILRB5"      
## [16] "ARFGEF3"      "ADAM23"       "MXI1"         "PATJ"         "PAM"         
## [21] "ST18"         "ZFYVE28"      "JAML"         "PLPP3"        "CAMK2N1"     
## [26] "SNED1"        "ARHGEF3"      "RANBP3L"      "STXBP6"       "TBC1D10C"    
## [31] "MCTP1"        "SRRM3"        "TMTC2"        "ADGRB1"       "FAM153CP"    
## [36] "AC093843.1"   "SATB1-AS1"    "DIRC3"        "TRHDE-AS1"    "LINC01322"   
## [41] "SELENOP"      "LINC01138"    "RP11-335E8.3"

## [1] 2
##  [1] "SLC4A7"       "ZNF532"       "TXNDC16"      "POLA1"        "VWA8"        
##  [6] "APBA1"        "TENT5A"       "SGK1"         "DTD1"         "RTN4IP1"     
## [11] "LANCL2"       "ERMN"         "ADAMTS17"     "FOXO1"        "PUS10"       
## [16] "SMIM14"       "SOCS6"        "PRDX6-AS1"    "ZNF433-AS1"   "RP13-188A5.1"
## [21] "TWIST2"       "LINC01278"    "ADAP1"        "KLHL24"       "FAM117B"     
## [26] "CCNG2"        "PELI2"        "AUH"          "PDK1"         "AGPAT5"      
## [31] "ETS2"         "MARCHF8"      "INSR"         "CEBPB"        "KCNE1"       
## [36] "IFNLR1"       "PLCG2"        "CEBPD"

## [1] 3
##  [1] "ABCB4"          "TTC7A"          "SYNDIG1"        "CPED1"         
##  [5] "FAM149A"        "TMEM156"        "PEBP4"          "GAREM1"        
##  [9] "ARL5C"          "RASGEF1C"       "TENM4"          "TMEM163"       
## [13] "DEPTOR"         "GHRL"           "LIPC"           "MICOS10"       
## [17] "MARCHF3"        "C5orf64"        "KBTBD12"        "TSBP1-AS1"     
## [21] "ZRANB2-AS2"     "FSIP2-AS1"      "RP11-634B7.4"   "LINC01141"     
## [25] "LINC01684"      "KCNMB2-AS1"     "LINC02008"      "XACT"          
## [29] "CTB-161M19.4"   "LINC02232"      "LINC01094"      "RP11-541P9.3"  
## [33] "RP11-946L16.1"  "RP11-493L12.4"  "RP11-399K21.11" "CH17-55D9.1"   
## [37] "RP11-685G11.1"  "NCMAP"          "GLDN"           "CCDC73"        
## [41] "MYO16-AS1"      "RP11-707P17.1"  "RP11-452F19.4"

## [1] 4
##  [1] "CEACAM1"                 "PLAGL1"                 
##  [3] "RAB38"                   "SPATA6"                 
##  [5] "ARMH4"                   "NKD1"                   
##  [7] "DISP1"                   "DENND2B"                
##  [9] "ATF7IP2"                 "DLEU1"                  
## [11] "CATSPERE"                "SPATA13_ENSG00000182957"
## [13] "SCFD2"                   "PRKN"                   
## [15] "MBD5"                    "AC007879.5"             
## [17] "FTCDNL1"                 "AC105760.2"             
## [19] "LINC01515"               "MIR646HG"               
## [21] "AC002539.1"              "RPL34-DT"               
## [23] "COX10-AS1"               "RNF217-AS1"             
## [25] "LINC01258"               "RP11-130F10.1"          
## [27] "LINC02762"               "RHOXF1-AS1"             
## [29] "RP11-323I15.5"           "LINC00907"              
## [31] "RP11-323P17.2"           "CCDC28A-AS1"            
## [33] "LINC01374"               "EIF1B-AS1"              
## [35] "RP11-692P14.1"           "RP4-545L17.11"          
## [37] "RP11-314E10.1"           "RNASET2"                
## [39] "ARHGAP6"                 "PILRA"                  
## [41] "GRK3"                    "BICRAL"                 
## [43] "PADI2"

## [1] 5
##  [1] "MTHFS"    "BRIP1"    "SCAI"     "ZNRF1"    "RANBP17"  "JARID2"  
##  [7] "NSMAF"    "MSR1"     "BCAT1"    "ZFAT"     "HACE1"    "TBC1D2"  
## [13] "INTS6"    "DOT1L"    "ARRDC2"   "UBE2R2"   "PPARD"    "GBE1"    
## [19] "PAPOLG"   "RLF"      "ESYT2"    "ELL2"     "TRIP10"   "PHF21A"  
## [25] "GLUL"     "GFOD1"    "MCPH1"    "RIT2"     "ASAP1"    "CFDP1"   
## [31] "CDCP1"    "PPIP5K1"  "AFF1"     "KLHL6"    "CHST15"   "GPRIN3"  
## [37] "RALGAPA2" "COL27A1"  "ZNF277"   "RGL3"

## [1] 6
##  [1] "ARHGEF18"                "ACYP2"                  
##  [3] "RP11-131L23.1"           "SLC16A1-AS1"            
##  [5] "XIST"                    "HMGA1P4"                
##  [7] "PVT1"                    "ATP6V0D1-DT"            
##  [9] "STAB1"                   "FAM50A"                 
## [11] "AK1"                     "GTDC1"                  
## [13] "KIAA0513"                "TIAM2"                  
## [15] "SLC2A13"                 "PARP8"                  
## [17] "CFAP161"                 "ST3GAL2"                
## [19] "TNFRSF11B"               "GREM1"                  
## [21] "CXXC5"                   "LPCAT4"                 
## [23] "POTEG"                   "ZNF407"                 
## [25] "AC023469.1"              "SNHG14"                 
## [27] "RP5-864K19.4"            "ARL17B"                 
## [29] "CYP1B1-AS1"              "LINC01762"              
## [31] "RP11-154D17.1"           "LINC01609"              
## [33] "CTB-41I6.2"              "MTRNR2L12"              
## [35] "RMRP_ENSG00000269900"    "SCARNA2_ENSG00000270066"
## [37] "LL22NC03-2H8.5"          "RP11-154H23.4"          
## [39] "CH507-513H4.1"           "CH507-528H12.1"         
## [41] "RP11-596C23.6"           "RP11-344F5.1"           
## [43] "AC003099.2"

## [1] 7
##  [1] "NEXMIF"        "ANGPT2"        "LIPG"          "NIPAL2"       
##  [5] "PLAT"          "ECM2"          "PODXL2"        "NEK11"        
##  [9] "AKAP7"         "PLAU"          "OMD"           "SGCE"         
## [13] "FMO5"          "PDE5A"         "RAB40B"        "MLIP"         
## [17] "IRAK1BP1"      "MMS22L"        "RNF180"        "MAMDC2"       
## [21] "TMEM52B"       "BEAN1"         "B3GLCT"        "COL5A2"       
## [25] "MAMDC2-AS1"    "LTC4S"         "ENTPD3-AS1"    "AC092431.3"   
## [29] "RP11-123B3.2"  "AC006160.5"    "MRPS30-DT"     "LIX1-AS1"     
## [33] "PRANCR"        "LINC02316"     "RP11-305E17.8" "RP11-6G22.1"  
## [37] "FSTL4"         "SERPINE1"      "GALNT18"       "ARSK"         
## [41] "SH3BGRL2"      "ARHGEF25"

## [1] 8
##  [1] "MUSK"          "MMP24"         "IER3"          "CH25H"        
##  [5] "DPYS"          "BEX3"          "H2AC20"        "SPDYE2"       
##  [9] "ANKUB1"        "MTCP1"         "DOCK4-AS1"     "AC023590.1"   
## [13] "ARHGAP26-AS1"  "ZNF451-AS1"    "RP11-165F24.3" "AC017101.10"  
## [17] "ALG13-AS1"     "AC083884.8"    "RP1-117O3.2"   "KCNMA1-AS1"   
## [21] "BCL2L1-AS1"    "RP11-544A12.4" "DENND6A-AS1"   "RP5-1101C3.1" 
## [25] "LINC00996"     "RP11-39E3.3"   "RP11-1H15.2"   "RP11-434H14.1"
## [29] "RP1-71H24.1"   "CTD-2647E9.3"  "RP11-317G6.1"  "RP11-106M3.3" 
## [33] "RNF213-AS1"    "PRKCA-AS1"     "RP11-737O24.2" "RP11-16C1.3"  
## [37] "TCF4-AS1"      "H2AC19"        "RP11-386I14.4" "RP11-1H15.4"  
## [41] "AC009505.4"    "CTD-2285E13.1"

## [1] 9
##  [1] "DERA"          "TYMP"          "NME3"          "PLGRKT"       
##  [5] "ENOSF1"        "IFI44L"        "HERC6"         "FHAD1"        
##  [9] "ENPP3"         "HESX1"         "ZDHHC19"       "FAM227B"      
## [13] "OLR1"          "ODF3B"         "MCMDC2"        "H2BC4"        
## [17] "MX2"           "TMSB4X"        "RP11-115J16.1" "OVCH1-AS1"    
## [21] "LINC02073"     "H2BC8"         "H2AC8"         "H2BC7"        
## [25] "RP1-111C20.3"  "SLC2A3"        "RGS1"          "TGFB2"        
## [29] "ITGB8"         "SRGN"          "RNF144B"       "TMEM140"      
## [33] "FRRS1"         "TAMALIN"       "ALDH1A1"       "APLF"         
## [37] "H1-0"          "AF064858.6"    "AC093818.1"    "PIK3IP1-DT"   
## [41] "IFITM10"       "RP11-13N12.1"

## [1] 10
##  [1] "ALDOC"         "BEX2"          "TET1"          "FBN2"         
##  [5] "BCL2A1"        "TNFRSF21"      "AIM2"          "MOBP"         
##  [9] "ABAT"          "NFIX"          "CD9"           "PLEKHH3"      
## [13] "ANO8"          "PGM1"          "PFKFB4"        "USP9Y"        
## [17] "KDM5B"         "NR4A3"         "HIF3A"         "KDM6B"        
## [21] "HILPDA"        "MYO1G"         "ADCY3"         "LYPD5"        
## [25] "CCDC107"       "G6PD"          "FBXO27"        "ANKZF1"       
## [29] "OTUD1"         "FRMD5"         "ADCY5"         "TRNAU1AP"     
## [33] "TNFAIP8L3"     "TBKBP1"        "TSPAN4"        "STARD10"      
## [37] "SLC12A8"       "LUCAT1"        "RP11-661A12.5"

## [1] 11
##  [1] "MBNL3"         "P3H2"          "PIGL"          "PUDP"         
##  [5] "GIPC2"         "GPAT3"         "IRF8"          "ARHGAP42"     
##  [9] "ADAMTS15"      "DNAJC24"       "TLN2"          "GAP43"        
## [13] "ZMAT3"         "PNMA3"         "CDIN1"         "SDHAF3"       
## [17] "FIRRE"         "ALOX12-AS1"    "RP11-535M15.1" "AC073115.7"   
## [21] "RP5-1198O20.4" "C12orf75"      "LINC00894"     "RP11-195C7.1" 
## [25] "AC073115.6"    "LINC00968"     "RP11-679C8.2"  "MIR3142HG"    
## [29] "MIR222HG"      "RP11-323F24.5" "RP11-111G13.1" "RGCC"         
## [33] "SLC25A37"      "SLC26A7"       "DHRS3"         "TLR5"         
## [37] "LINC02397"     "GCC2-AS1"      "AC025171.1"    "MYOCOS"       
## [41] "RP11-249L21.6"

## [1] 12
##  [1] "PDE10A"        "IGSF11"        "TMEM44"        "BEND6"        
##  [5] "LINC00476"     "FIGN"          "ZNF804B"       "DOK6"         
##  [9] "RP11-673E1.1"  "PSMD7-DT"      "RP11-640F22.1" "LINC02885"    
## [13] "RP11-320L2.1"  "ADGRL1"        "COL5A3"        "CDH20"        
## [17] "DNAH6"         "CHD5"          "CSMD2"         "PXDNL"        
## [21] "PALM2AKAP2"    "ANKRD30BL"     "PRICKLE2"      "ADGRV1"       
## [25] "AMER2"         "PDZRN4"        "FSTL5"         "GPC5"         
## [29] "SSTR2"         "SLIT1"         "CR1L"          "RORB"         
## [33] "LINC00970"     "BASP1-AS1"     "RP11-191L9.4"  "RP11-147G16.1"
## [37] "RP11-696N14.1" "RP11-17A1.3"   "RP11-259O2.1"  "LINC01414"    
## [41] "CTC-535M15.2"  "RP11-436D23.1" "LINC00551"

## [1] 13
##  [1] "RP4-809F18.1"  "MRC1"          "SYT7"          "PCDH11Y"      
##  [5] "FGF14"         "ATP8A1"        "ATP8A2"        "ZNF365"       
##  [9] "RBMS3"         "STXBP5L"       "TENM2"         "CNTN5"        
## [13] "ADGRL3"        "ZNF385D"       "SPOCK1"        "NCAM2"        
## [17] "CLSTN2"        "GABRB1"        "CSMD3"         "LRFN5"        
## [21] "SEMA3E"        "FUT9"          "LRRC3B"        "KCTD16"       
## [25] "FLRT2"         "PTPRT"         "TAFA2"         "ZNF521"       
## [29] "LINC00632"     "MIAT"          "LINC01320"     "LINC01435"    
## [33] "SHISA9"        "RP11-384F7.2"  "SLC5A4-AS1"    "CPEB2-DT"     
## [37] "RP11-79E3.2"   "RP11-20D14.3"  "LINC00558"     "U91319.1"     
## [41] "IQCJ-SCHIP1"   "RP4-799O8.1"   "RP11-398J12.1"

## [1] 14
##  [1] "BCAS3"         "NUBPL"         "B2M"           "FTH1"         
##  [5] "XKR6"          "RTTN"          "ARSJ"          "ZFP36L1"      
##  [9] "RPL41"         "SLC1A3"        "IRAK3"         "SLC26A3"      
## [13] "ANKRD12"       "PRKAG2"        "RAPGEF1"       "CTSD"         
## [17] "HS3ST2"        "PTPRE"         "SOX5"          "CPM"          
## [21] "SSH2"          "SDK1"          "ARID5B"        "MERTK"        
## [25] "FMNL2"         "CDC42SE2"      "CLASP2"        "OXR1"         
## [29] "ABCA1"         "MTSS1"         "BNC2"          "CHD2"         
## [33] "BAIAP2"        "OPCML"         "AS3MT"         "AC013463.2"   
## [37] "NEAT1"         "RP11-368L12.1" "RP5-1015P16.1" "RENO1"

## [1] 15
##  [1] "LDAH"         "TEX9"         "MTHFD2L"      "TAGAP"        "KIF5C-AS1"   
##  [6] "MTRNR2L8"     "MYO9A"        "CERS4"        "MAP3K20"      "CEP170B"     
## [11] "KATNAL1"      "STN1"         "SNX25"        "SEM1"         "AFDN"        
## [16] "DNAJB2"       "DRAM1"        "PGGHG"        "NR6A1"        "RSU1"        
## [21] "LRRC4C"       "CLEC1A"       "BTBD11"       "AMN1"         "PITPNC1"     
## [26] "FBXO32"       "NEK10"        "KLF13"        "RESF1"        "ZHX2"        
## [31] "PARVB"        "CTD-3088G3.8" "IARS1"        "TOX"          "LINC00862"   
## [36] "ZDBF2"        "C17orf67"     "SGO1-AS1"     "RP11-305L7.3" "CLEC5A"      
## [41] "C2orf27A"

## [1] 16
##  [1] "IPCEF1"        "RBL1"          "ARSB"          "IFT43"        
##  [5] "METTL25"       "CGNL1"         "TBC1D14"       "FRMD6"        
##  [9] "ITGA9"         "C11orf49"      "LRRC8C"        "RAB39A"       
## [13] "RNLS"          "RTN4RL1"       "ERC2"          "CENPP"        
## [17] "LIN52"         "RP11-736I24.5" "CELSR3"        "CLEC16A"      
## [21] "LCP2"          "DOCK3"         "E2F3"          "FRMD4B"       
## [25] "HELLS"         "RASSF8"        "PRAM1"         "WNT2B"        
## [29] "PPFIA2"        "SH3RF1"        "SAMD12"        "SERTAD2"      
## [33] "AIDA"          "SYCP2"         "ROR1-AS1"      "AC092835.2"   
## [37] "LINC02646"     "FMN1"          "HCG17"         "RP11-114N19.3"
## [41] "RP11-404C6.6"

## [1] 17
##  [1] "PKD2L2"                  "ATP8B1"                 
##  [3] "PCSK1N"                  "CALY"                   
##  [5] "MCTP2"                   "ADAMTS19"               
##  [7] "RAB37"                   "IRAG1-AS1"              
##  [9] "TMEM151B"                "EYS"                    
## [11] "FSIP2"                   "CARNMT1-AS1"            
## [13] "SMCR5"                   "AC105461.1"             
## [15] "PCDH9-AS2"               "LINC01277"              
## [17] "RP3-525N10.2"            "RP1-225E12.2"           
## [19] "COA6-AS1"                "ARHGAP15-AS1"           
## [21] "LANCL1-AS1"              "RMDN2-AS1"              
## [23] "KDM4A-AS1"               "LRIG2-DT"               
## [25] "LINC01877"               "RP11-544A12.8"          
## [27] "ALG1L9P_ENSG00000248671" "CTD-2537O9.1"           
## [29] "RP11-571M6.7"            "RP11-66H6.3"            
## [31] "LINC00621"               "CTD-3149D2.4"           
## [33] "RP4-769N13.7"            "COPG2IT1"               
## [35] "RP11-237N2.1"            "RP11-65F13.4"           
## [37] "RP11-685G9.5"            "RP11-617F9.2"           
## [39] "RP11-399K19.1"           "RASGRP2"                
## [41] "OLFM1"                   "H1-10"                  
## [43] "CCDC71L"                 "RP11-322M13.1"

## [1] 18
##  [1] "SNCAIP"   "TRPM3"    "MPP2"     "GNLY"     "CHN1"     "RALGPS1" 
##  [7] "MEIS1"    "TRPC1"    "SYCE2"    "CNTN1"    "NCDN"     "CELF4"   
## [13] "CPE"      "GABRG2"   "KCNH1"    "CDH18"    "CACNA1B"  "CRIM1"   
## [19] "ME3"      "HOMER1"   "SCN3A"    "CACNA2D1" "PTPRN2"   "FMN2"    
## [25] "SYN2"     "SPTBN4"   "EDIL3"    "GRM5"     "ZFPM2"    "CNTNAP2" 
## [31] "PPM1E"    "CDH4"     "UNC5C"    "TSHZ2"    "PBX1"     "SYN3"    
## [37] "MYT1L"    "GRM7"     "MIB2"

## [1] 19
##  [1] "PRKCQ"   "SLC26A4" "NLRP1"   "PRTFDC1" "DAAM1"   "PEX7"    "WLS"    
##  [8] "DOCK10"  "ZNF707"  "HRH1"    "HECW1"   "SAMD4A"  "PRKCH"   "WWC3"   
## [15] "LIMCH1"  "RFX3"    "RFX2"    "DOCK9"   "FNDC3A"  "NHSL1"   "SEMA6D" 
## [22] "MAP3K6"  "USP53"   "DIXDC1"  "EPB41"   "STXBP5"  "SLC43A2" "LDLRAD4"
## [29] "DHRSX"   "CRADD"   "TMEM51"  "MALT1"   "LRFN4"   "PACS1"   "SLC35E3"
## [36] "CARD11"  "SLC48A1" "FADS3"   "MICAL3"

## [1] 20
##  [1] "OSBPL6"   "GCNT2"    "PARD3B"   "RALGPS2"  "MIS18BP1" "EPHB2"   
##  [7] "SLC22A23" "SMAD6"    "STAMBPL1" "AIG1"     "CD226"    "MAGI1"   
## [13] "PTPN14"   "BACH1"    "TIAM1"    "PLEKHA7"  "NXN"      "S100Z"   
## [19] "MBOAT1"   "SH3RF3"   "NCKAP5"   "DNAH14"   "TNFRSF1B" "PLEKHA5" 
## [25] "RASSF2"   "DENND1A"  "SLC35E1"  "ZBTB46"   "STARD13"  "AGAP3"   
## [31] "DENND4C"  "FNBP1L"   "SLC2A5"   "SRSF12"   "AGAP1"    "RBFOX3"  
## [37] "FAM110B"  "TANC2"    "PELI1"    "SIPA1L1"

## [1] 21
##  [1] "PDK4"     "TMSB10"   "PER3"     "SLC4A8"   "DHRS9"    "EFR3B"   
##  [7] "ITPR2"    "NRN1"     "ABCC4"    "C3"       "IL6ST"    "LPAR6"   
## [13] "PIGK"     "KIF26B"   "TMEM169"  "P2RY12"   "EMB"      "CMKLR1"  
## [19] "ATAD5"    "CA8"      "KIAA0825" "VKORC1L1" "LPAR1"    "ATP9A"   
## [25] "NEBL"     "SLC16A10" "LIFR"     "FAM162A"  "SLC6A8"   "KCNK1"   
## [31] "TTYH3"    "TMEM63B"  "SLC12A6"  "ATP8B2"   "SSBP3"    "SPRY1"   
## [37] "GPRC5C"   "PEAK1"    "MAMDC4"   "DGAT1"

## [1] 22
##  [1] "HTR2B"         "UBE2Q2"        "ST3GAL1"       "FAM107B"      
##  [5] "HDHD5"         "PDE8A"         "GRAMD4"        "PPP1R15A"     
##  [9] "GALNT16"       "RNF24"         "RNMT"          "BNIP3L"       
## [13] "APBB3"         "MGAT1"         "CHI3L1"        "BTG1"         
## [17] "RGS16"         "MYO10"         "ARHGAP18"      "PLIN2"        
## [21] "HTR7"          "ACSL1"         "RASSF3"        "CFAP251"      
## [25] "RHOBTB3"       "NFIL3"         "DDIT4"         "PPP1R3B"      
## [29] "BNIP3"         "FAM210A"       "MITF"          "CD55"         
## [33] "ERO1A"         "CD247"         "LILRB3"        "XKR9"         
## [37] "ZSCAN31"       "AF064858.8"    "AC002066.1"    "USP2-AS1"     
## [41] "SBF2-AS1"      "RP11-429A20.3"

## [1] 23
##  [1] "ETV1"    "OSBPL5"  "MGLL"    "RPH3A"   "PITPNM2" "PDE4D"   "PSD3"   
##  [8] "IER2"    "CPLX1"   "ATF5"    "SKA2"    "PKD1"    "CDK14"   "CDK17"  
## [15] "PDE4A"   "CTNNA2"  "RAB27A"  "FERMT2"  "TNS1"    "NPDC1"   "SASH1"  
## [22] "CCND3"   "HPCAL1"  "MOB3B"   "IQSEC2"  "DOCK6"   "ZNF331"  "SNAP25" 
## [29] "IQSEC1"  "NEK7"    "SORCS3"  "LRP1B"   "ALOX15B" "ZDHHC20" "CADM1"  
## [36] "PCDH9"   "PDE4B"   "RALYL"   "OSBP2"   "UNC13B"

## [1] 24
##  [1] "ERCC8"                     "CECR2"                    
##  [3] "SUSD1"                     "MAP2K6"                   
##  [5] "CCDC18"                    "ITM2C"                    
##  [7] "GAS2L3"                    "LRIG1"                    
##  [9] "PLAC8"                     "SLC25A25"                 
## [11] "PSTPIP2"                   "CLIC2"                    
## [13] "UCN"                       "C1QA"                     
## [15] "PTPN2"                     "AATK"                     
## [17] "APOO"                      "LEKR1"                    
## [19] "LINC01605_ENSG00000253161" "RP11-154H12.3"            
## [21] "RP4-681L3.3"               "HGF"                      
## [23] "FNDC3B"                    "TRIP11"                   
## [25] "MTMR8"                     "TIMP1"                    
## [27] "MICU1"                     "TGFBI"                    
## [29] "KIF1A"                     "FCHO1"                    
## [31] "UBAP2"                     "DUSP10"                   
## [33] "GUK1"                      "PCNT"                     
## [35] "IL15"                      "CLIC4"                    
## [37] "GLRX"                      "GOLIM4"                   
## [39] "LIMK2"                     "SKIV2L"                   
## [41] "FMNL1-DT"

## [1] 25
##  [1] "RPL3"     "RPL18A"   "RPL19"    "RPL34"    "RPL24"    "IFIT3"   
##  [7] "IFIT2"    "CCDC170"  "ATP5F1E"  "FGF13"    "RPLP1"    "RPS24"   
## [13] "PRDM5"    "RPS2"     "RPS11"    "RPL11"    "SPAG16"   "RPL32"   
## [19] "FAU"      "ATG10"    "RPL26"    "ELAVL4"   "NFIA"     "RPL38"   
## [25] "RPLP2"    "IFIT1"    "RPS23"    "CPNE4"    "RPL12"    "RPL23A"  
## [31] "RPL39"    "RORA-AS1" "MMP28"    "SPOCK2"   "SLC1A2"   "CCNH"    
## [37] "ZMAT4"    "CMSS1"    "ADARB1"

## [1] 26
##  [1] "FOLR2"         "C11orf65"      "GLIPR1L1"      "DLEU7"        
##  [5] "ENO4"          "FAM177B"       "LINC01285"     "HNRNPA1P48"   
##  [9] "EDNRB-AS1"     "LINC01375"     "SLC8A1-AS1"    "RP11-526K17.2"
## [13] "WEE2-AS1"      "HCG22"         "RP11-142M10.2" "SRGAP2-AS1"   
## [17] "RNASEH2B-AS1"  "RP11-353M9.1"  "RP11-666F17.1" "RP11-142A5.1" 
## [21] "RP11-712B9.2"  "RP11-360F5.1"  "CTD-2227I18.1" "RP11-238K6.1" 
## [25] "RP11-624C23.1" "RP11-649G15.2" "RP11-463D19.1" "RP11-513G19.1"
## [29] "RP11-136F16.1" "RP11-370I10.2" "RP11-517O13.1" "LMO7-AS1"     
## [33] "ABHD15-AS1"    "RP11-354K4.2"  "RP11-74J13.8"  "CERNA2"       
## [37] "RP1-80B9.4"    "RP11-264E23.4" "RP11-7F3.1"    "AC009166.9"   
## [41] "RP11-56I23.2"  "CTD-2021K4.2"  "RP3-467L1.4"

## [1] 27
##  [1] "ACER3"       "EPDR1"       "OGN"         "MAP3K8"      "SLC2A9"     
##  [6] "GALNT12"     "FLVCR2"      "SLC10A7"     "SIRPD"       "XAF1"       
## [11] "EPSTI1"      "PTH2R"       "AOPEP"       "LY96"        "MAP3K7CL"   
## [16] "RAB28"       "TNFRSF13C"   "PBX3"        "WDR25"       "PGBD5"      
## [21] "PROS1"       "MS4A4E"      "LINC00630"   "CCDC26"      "CDKN2B-AS1" 
## [26] "LINC02432"   "C5orf17"     "C8orf37-AS1" "LINC02328"   "LINC01146"  
## [31] "RP11-38B6.1" "RP13-52K8.2" "CDH26"       "SEC14L1"     "CHSY1"      
## [36] "TLR2"        "NGLY1"       "CYRIA"       "GK"          "UBXN2B"     
## [41] "MIR181A1HG"

## [1] 28
##  [1] "IL7"            "NEURL2"         "LILRB2"         "MIR4435-2HG"   
##  [5] "RP11-575L7.8"   "CPB2-AS1"       "STARD4-AS1"     "ANK2-AS1"      
##  [9] "RP11-511B23.2"  "RP11-638I2.8"   "RP11-126O1.4"   "RP11-793H13.14"
## [13] "RP11-622I12.1"  "RP11-275G7.2"   "RP11-261A24.1"  "RP1-18C9.3"    
## [17] "HIVEP2"         "MAMLD1"         "GADD45B"        "IL4I1"         
## [21] "TREM1"          "CEMIP2"         "GPNMB"          "NIBAN2"        
## [25] "RASGEF1B"       "IER5"           "VMO1"           "ADSS1"         
## [29] "ANKRD37"        "ZNF395"         "TPRG1"          "LINC00910"     
## [33] "H2BU1"          "FAM229A"        "LIMD1-AS1"      "DARS1-AS1"     
## [37] "RP11-47I22.3"   "MIR155HG"       "RP11-384C4.7"   "LINC02698"     
## [41] "HIF1A-AS3"      "SAP30-DT"       "RP11-475M20.2"  "RP11-134L10.2"

## [1] 29
##  [1] "LRRC6"         "BEX1"          "UNC80"         "AC011288.2"   
##  [5] "LINC00923"     "FAM66D"        "CEROX1"        "TENM1"        
##  [9] "LRRC7"         "ZFY"           "ARHGAP10"      "TRHDE"        
## [13] "SESN1"         "RAPGEF4"       "NALCN"         "KCNT1"        
## [17] "PCSK2"         "EMILIN2"       "PDZD2"         "CBLN2"        
## [21] "NPAS3"         "AK5"           "NLGN1"         "CTNND2"       
## [25] "NEGR1"         "HPSE2"         "CADM2"         "RIMS2"        
## [29] "RBM44"         "NRXN1"         "NELL2"         "LSAMP"        
## [33] "NRG3"          "NPIPB15"       "CACNA1E"       "FAM155A"      
## [37] "MEG3"          "RP11-37N22.1"  "AC067959.1"    "RP11-657O9.1" 
## [41] "CTC-340A15.2"  "RMST"          "RP11-111A21.1"

## [1] 30
##  [1] "MCF2L2"        "CARMIL1"       "LRRC74A"       "PROCR"        
##  [5] "CST3"          "PLEK"          "PIGC"          "DUOX1"        
##  [9] "MED12L"        "AGBL3"         "C1QC"          "BTG2"         
## [13] "PAQR3"         "SHOC1"         "FILIP1L"       "SLC35G2"      
## [17] "DTWD2"         "H2BC18"        "AIF1"          "RP11-321C24.1"
## [21] "ENTPD1-AS1"    "RP4-568F9.6"   "IPO9-AS1"      "RP5-1132H15.1"
## [25] "LINC00960"     "CTD-3239E11.2" "RP11-452H21.1" "RP11-867G2.8" 
## [29] "CEACAM16-AS1"  "KCNQ1OT1"      "TSIX"          "MIR223HG"     
## [33] "LINC00624"     "RP11-458A7.1"  "RP11-13J12.3"  "PDGFB"        
## [37] "COL5A1"        "DHRS13"        "MFSD4B"        "H2AC6"        
## [41] "CTD-2643I7.5"

## [1] 31
##  [1] "SP140"         "AZIN2"         "BANK1"         "C4orf19"      
##  [5] "ADGRG5"        "GASK1B"        "PLD4"          "TMC7"         
##  [9] "MIR31HG"       "CYSLTR1"       "PLCXD3"        "CLEC9A"       
## [13] "LINC01357"     "LINC00539"     "LINC02642"     "LINC00884"    
## [17] "RP11-120D5.1"  "PTCHD4"        "LINC02211"     "MIR4300HG"    
## [21] "GPRC5D-AS1"    "LINC02057"     "LINC01091"     "AC008697.1"   
## [25] "ZFPM2-AS1"     "RP11-745L13.2" "CTC-575N7.1"   "MAILR"        
## [29] "RP11-10H3.1"   "SMIM35"        "RP11-630C16.2" "RP11-554D14.6"
## [33] "LINC02444"     "RP11-588H23.3" "RP11-72M17.1"  "RP11-187O7.3" 
## [37] "LINC02712"     "RP11-495L19.1" "RP11-437L7.2"  "RP11-622O11.6"
## [41] "RP11-168F24.3" "RP1-236J16.3"  "RP11-4F5.3"

## [1] 32
##  [1] "TPD52"   "ABCG2"   "STON2"   "RNF157"  "MYO5B"   "TSPYL2"  "FGR"    
##  [8] "MATK"    "TGFBR3"  "ATP1B3"  "MLF2"    "IL27RA"  "POU6F2"  "HAVCR1" 
## [15] "CYTIP"   "EPHA4"   "SLC2A1"  "GNA13"   "HSPH1"   "ELK1"    "SLC41A2"
## [22] "FGF2"    "LARP1B"  "GNA12"   "SNTG1"   "ADD3"    "RNF144A" "RASGRP3"
## [29] "MSI2"    "LONRF1"  "MYO1E"   "FGF17"   "PTMS"    "ZNF143"  "PRKCB"  
## [36] "LPL"     "EFNA5"   "SOGA3"   "ITGB3"

## [1] 33
##  [1] "CALCR"         "IGF1"          "PRDM11"        "MTERF1"       
##  [5] "TMEM241"       "NPL"           "SLC49A4"       "KCNMB1"       
##  [9] "LINC00467"     "SAMSN1"        "KCNMA1"        "AUTS2"        
## [13] "CX3CR1"        "ZNF608"        "MT1E"          "GPR34"        
## [17] "SPTLC3"        "FGGY"          "CAPS2"         "RP11-445F6.2" 
## [21] "TEX41"         "RP11-162D16.2" "LINC00271"     "RFX3-AS1"     
## [25] "UFL1-AS1"      "LINC01376"     "BDNF-AS"       "LINC01184"    
## [29] "RP11-319G6.1"  "RP11-381K20.2" "RP11-692D12.1" "ZNF10"        
## [33] "RP11-370I10.6" "RP11-281A20.2" "RP11-19D22.1"  "TMED8"        
## [37] "DARS1"         "OGFRL1"        "ABCG1"         "TMEM65"       
## [41] "LONRF3"        "ZC3H6"

## [1] 34
##  [1] "ANGPTL1"       "SLC5A9"        "ADGRG2"        "INSYN2B"      
##  [5] "AC002463.3"    "ELMO1-AS1"     "TMLHE-AS1"     "AC096558.1"   
##  [9] "AC037445.1"    "RP11-528G1.2"  "MYCBP2-AS1"    "DIAPH2-AS1"   
## [13] "CCDC200"       "AC018890.6"    "RP11-775D22.3" "ZBTB20-AS5"   
## [17] "MEF2C-AS2"     "CTD-2015H6.3"  "RHOQ-AS1"      "RP11-268P4.5" 
## [21] "RP11-506H20.1" "AP000487.6"    "RP11-196H14.2" "RP11-493L12.3"
## [25] "RP11-713N11.4" "USP3-AS1"      "RP11-815J21.4" "RP11-16B9.1"  
## [29] "RP11-621L6.2"  "RP11-703M24.5" "RP11-793A3.2"  "RP11-58G13.1" 
## [33] "RP11-53B2.3"   "RP1-256G22.2"  "CTD-2282P23.2" "RP11-121C2.3" 
## [37] "LINC02666"     "DISC2"         "RP11-314L11.1" "GS1-98E2.1"   
## [41] "RP11-21M24.6"  "RP11-1146N6.3" "RP11-555K12.4" "NRG2"

## [1] 35
##  [1] "PLPP1"         "HAMP"          "ADGRD1"        "CYREN"        
##  [5] "SSPN"          "ACKR4"         "ARHGAP20"      "WDPCP"        
##  [9] "SLC9B1"        "TMEM144"       "GPR85"         "NLGN4Y"       
## [13] "CYTL1"         "B3GNT5"        "TTTY14"        "FLJ40194"     
## [17] "PCED1B"        "SCOC-AS1"      "LINC02649"     "AC003090.1"   
## [21] "RP11-202G18.1" "AC007682.1"    "RAP2C-AS1"     "RP11-557H15.4"
## [25] "ITGA9-AS1"     "FBXO30-DT"     "RP11-246A10.1" "ARHGAP8"      
## [29] "RP11-796E2.4"  "FAM198B-AS1"   "RP11-281P23.2" "LINC02742"    
## [33] "RP11-37B2.1"   "RP11-486A14.2" "RP11-516C1.1"  "CTD-2336H13.2"
## [37] "LINC01572"     "ZNF528-AS1"    "RP11-419I17.1" "RP11-574F11.4"
## [41] "RP6-91H8.6"    "RP11-221G19.1" "RP11-321P16.3"

## [1] 36
##  [1] "PFN2"     "ABCC1"    "ABCA5"    "DENND5B"  "GTF2IRD1" "VCAN"    
##  [7] "ABCA7"    "KCNAB2"   "CPSF1"    "RAP1GAP"  "ZNF586"   "ITPKC"   
## [13] "MYOM1"    "NDFIP2"   "FLT1"     "DGKH"     "HSF4"     "CLIP4"   
## [19] "TSHZ3"    "ZC4H2"    "HIP1"     "SH3BP5"   "RAMP1"    "MACROD1" 
## [25] "MICAL2"   "GDF11"    "PLXNC1"   "CPNE8"    "RPP38"    "CAMK4"   
## [31] "ACOT11"   "GMEB1"    "ATOH8"    "FRMD3"    "C11orf80" "JAKMIP2" 
## [37] "ZBTB7A"   "ZBTB7C"   "SESTD1"   "NHEJ1"

## [1] 37
##  [1] "SCMH1"         "ADAM28"        "ST6GAL1"       "CENPK"        
##  [5] "FOXP2"         "PCBD2"         "GARNL3"        "GSTCD"        
##  [9] "EFCAB11"       "FRMD4A"        "ANO10"         "ARHGAP25"     
## [13] "NMNAT3"        "SFMBT1"        "PRMT9"         "NAALADL2"     
## [17] "SLC9A9"        "DYNC2H1"       "SRGAP3"        "KCNMB2"       
## [21] "SFMBT2"        "CCDC7"         "MEI4"          "SCIN"         
## [25] "ARHGAP15"      "CTTNBP2"       "LAPTM4B"       "CLNK"         
## [29] "FOXP1"         "HPCAL4"        "FAM13A"        "CSGALNACT1"   
## [33] "FER"           "JAZF1"         "ADK"           "ROBO1"        
## [37] "RNF150"        "MSRA"          "MAML2"         "GDI1"         
## [41] "RP11-351A11.1"

## [1] 38
##  [1] "ICA1"          "OPHN1"         "CASS4"         "GPATCH2"      
##  [5] "CD69"          "IL1A"          "RCAN3"         "ZRANB3"       
##  [9] "IL1B"          "NRGN"          "TSPAN7"        "CACNA1D"      
## [13] "PLXDC1"        "CCDC171"       "MACROD2"       "KCNIP1"       
## [17] "CACNB4"        "COL25A1"       "LIPE-AS1"      "STX18-AS1"    
## [21] "MIR100HG"      "RP11-160E2.6"  "RP11-413N10.3" "ADAM22"       
## [25] "NCS1"          "NCOA7"         "CLVS2"         "CACNA1C"      
## [29] "MAPK13"        "DLGAP1"        "KCND3"         "DPP10"        
## [33] "CSMD1"         "KCND2"         "ANKS1B"        "PRKG1"        
## [37] "KCNIP4"        "MAGI2"         "KAZN"          "RYR2"

## [1] 39
##  [1] "ZFP64"         "NAV3"          "APBB1IP"       "TRIM2"        
##  [5] "PLCL1"         "CFAP74"        "GASK1A"        "SESN3"        
##  [9] "SETBP1"        "NAV2"          "ZDHHC14"       "TCERG1L"      
## [13] "SLC8A1"        "KCNQ3"         "ATP6AP1L"      "MIR99AHG"     
## [17] "LINC01356"     "TMEM72-AS1"    "RP1-30E17.2"   "CTA-292E10.6" 
## [21] "LMCD1-AS1"     "KIF9-AS1"      "AC097721.2"    "HDAC2-AS2"    
## [25] "MEF2C-AS1"     "GMDS-DT"       "LINC01301"     "LINC02055"    
## [29] "LINC00506"     "KCNQ2"         "CUX2"          "WDR45B"       
## [33] "HTR1E"         "FUT10"         "KCNQ5"         "ZNF846"       
## [37] "LNCAROD"       "KLF3-AS1"      "RP1-179N16.6"  "MTRNR2L1"     
## [41] "RP11-81K2.1"   "RP11-396B14.2" "RP11-358F13.1"

## [1] 40
##  [1] "HHAT"          "STS"           "ZNF821"        "GDAP1"        
##  [5] "MS4A4A"        "ADGRG6"        "F13A1"         "ZSCAN5A"      
##  [9] "AHI1"          "ABCA8"         "CDYL2"         "GLYATL1"      
## [13] "GRIK1"         "RFLNA"         "LINC02884"     "LINC02196"    
## [17] "LINC00639"     "DISC1FP1"      "RP11-341N18.1" "RP11-120L14.1"
## [21] "GCLC"          "GCLM"          "ARAP2"         "SLC9A7"       
## [25] "MEGF9"         "DCUN1D4"       "GYPC"          "RGL1"         
## [29] "CAMKMT"        "TNFAIP8"       "THRB"          "RASA2"        
## [33] "STARD9"        "GPHN"          "SH3PXD2B"      "ARL4C"        
## [37] "DPYD"          "EFCAB2"        "DENND1B"       "AGBL1"

for(n1 in names(goseq_res)){
  k = as.numeric(gsub("set_", "", n1))
  print(n1)
  print(gene_sets[[k]])
  print(goseq_res[[n1]])

}
## [1] "set_7"
##  [1] "NEXMIF"        "ANGPT2"        "LIPG"          "NIPAL2"       
##  [5] "PLAT"          "ECM2"          "PODXL2"        "NEK11"        
##  [9] "AKAP7"         "PLAU"          "OMD"           "SGCE"         
## [13] "FMO5"          "PDE5A"         "RAB40B"        "MLIP"         
## [17] "IRAK1BP1"      "MMS22L"        "RNF180"        "MAMDC2"       
## [21] "TMEM52B"       "BEAN1"         "B3GLCT"        "COL5A2"       
## [25] "MAMDC2-AS1"    "LTC4S"         "ENTPD3-AS1"    "AC092431.3"   
## [29] "RP11-123B3.2"  "AC006160.5"    "MRPS30-DT"     "LIX1-AS1"     
## [33] "PRANCR"        "LINC02316"     "RP11-305E17.8" "RP11-6G22.1"  
## [37] "FSTL4"         "SERPINE1"      "GALNT18"       "ARSK"         
## [41] "SH3BGRL2"      "ARHGEF25"     
## $reactome
##                       category over_represented_pvalue under_represented_pvalue
## 241 dissolution of fibrin clot             3.01944e-05                        1
##     numDEInCat numInCat        FDR
## 241          3        3 0.03568978
## 
## [1] "set_9"
##  [1] "DERA"          "TYMP"          "NME3"          "PLGRKT"       
##  [5] "ENOSF1"        "IFI44L"        "HERC6"         "FHAD1"        
##  [9] "ENPP3"         "HESX1"         "ZDHHC19"       "FAM227B"      
## [13] "OLR1"          "ODF3B"         "MCMDC2"        "H2BC4"        
## [17] "MX2"           "TMSB4X"        "RP11-115J16.1" "OVCH1-AS1"    
## [21] "LINC02073"     "H2BC8"         "H2AC8"         "H2BC7"        
## [25] "RP1-111C20.3"  "SLC2A3"        "RGS1"          "TGFB2"        
## [29] "ITGB8"         "SRGN"          "RNF144B"       "TMEM140"      
## [33] "FRRS1"         "TAMALIN"       "ALDH1A1"       "APLF"         
## [37] "H1-0"          "AF064858.6"    "AC093818.1"    "PIK3IP1-DT"   
## [41] "IFITM10"       "RP11-13N12.1" 
## $reactome
##                                                                               category
## 244                                      dna damage telomere stress induced senescence
## 9    activated pkn1 stimulates transcription of ar androgen receptor regulated genes k
## 76                            assembly of the orc complex at the origin of replication
## 89                                              base excision repair ap site formation
## 247                                                                    dna methylation
## 293                        ercc6 csb and ehmt2 g9a positively regulate rrna expression
## 453                                        inhibition of dna recombination at telomere
## 789  recognition and association of dna glycosylase with site containing an affected p
## 863                                                          rho gtpases activate pkns
## 1016                                        sirt1 negatively regulates rrna expression
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 244             1.044623e-06                1.0000000          5        9
## 9               2.618321e-05                0.9999995          4        8
## 76              2.618321e-05                0.9999995          4        8
## 89              2.618321e-05                0.9999995          4        8
## 247             2.618321e-05                0.9999995          4        8
## 293             2.618321e-05                0.9999995          4        8
## 453             2.618321e-05                0.9999995          4        8
## 789             2.618321e-05                0.9999995          4        8
## 863             2.618321e-05                0.9999995          4        8
## 1016            2.618321e-05                0.9999995          4        8
##              FDR
## 244  0.001234744
## 9    0.002634916
## 76   0.002634916
## 89   0.002634916
## 247  0.002634916
## 293  0.002634916
## 453  0.002634916
## 789  0.002634916
## 863  0.002634916
## 1016 0.002634916
## 
## [1] "set_23"
##  [1] "ETV1"    "OSBPL5"  "MGLL"    "RPH3A"   "PITPNM2" "PDE4D"   "PSD3"   
##  [8] "IER2"    "CPLX1"   "ATF5"    "SKA2"    "PKD1"    "CDK14"   "CDK17"  
## [15] "PDE4A"   "CTNNA2"  "RAB27A"  "FERMT2"  "TNS1"    "NPDC1"   "SASH1"  
## [22] "CCND3"   "HPCAL1"  "MOB3B"   "IQSEC2"  "DOCK6"   "ZNF331"  "SNAP25" 
## [29] "IQSEC1"  "NEK7"    "SORCS3"  "LRP1B"   "ALOX15B" "ZDHHC20" "CADM1"  
## [36] "PCDH9"   "PDE4B"   "RALYL"   "OSBP2"   "UNC13B" 
## $reactome
##                                          category over_represented_pvalue
## 203                               darpp 32 events            1.935443e-05
## 6    acetylcholine neurotransmitter release cycle            1.268236e-04
## 641 norepinephrine neurotransmitter release cycle            1.268236e-04
##     under_represented_pvalue numDEInCat numInCat        FDR
## 203                1.0000000          3        3 0.02287693
## 6                  0.9999986          3        5 0.04996849
## 641                0.9999986          3        5 0.04996849
## 
## [1] "set_25"
##  [1] "RPL3"     "RPL18A"   "RPL19"    "RPL34"    "RPL24"    "IFIT3"   
##  [7] "IFIT2"    "CCDC170"  "ATP5F1E"  "FGF13"    "RPLP1"    "RPS24"   
## [13] "PRDM5"    "RPS2"     "RPS11"    "RPL11"    "SPAG16"   "RPL32"   
## [19] "FAU"      "ATG10"    "RPL26"    "ELAVL4"   "NFIA"     "RPL38"   
## [25] "RPLP2"    "IFIT1"    "RPS23"    "CPNE4"    "RPL12"    "RPL23A"  
## [31] "RPL39"    "RORA-AS1" "MMP28"    "SPOCK2"   "SLC1A2"   "CCNH"    
## [37] "ZMAT4"    "CMSS1"    "ADARB1"  
## $reactome
##                                              category over_represented_pvalue
## 138                   cellular response to starvation                       0
## 301                 eukaryotic translation elongation                       0
## 302                 eukaryotic translation initiation                       0
## 452                               influenza infection                       0
## 557         metabolism of amino acids and derivatives                       0
## 640                       nonsense mediated decay nmd                       0
## 801       regulation of expression of slits and robos                       0
## 850 response of eif2ak4 gcn2 to amino acid deficiency                       0
## 901                                   rrna processing                       0
## 927                       selenoamino acid metabolism                       0
##     under_represented_pvalue numDEInCat numInCat FDR
## 138                        1         19       26   0
## 301                        1         19       23   0
## 302                        1         19       23   0
## 452                        1         19       27   0
## 557                        1         19       41   0
## 640                        1         19       23   0
## 801                        1         19       27   0
## 850                        1         19       25   0
## 901                        1         19       25   0
## 927                        1         19       26   0
## 
## $go_bp
##                                category over_represented_pvalue
## 630             cytoplasmic translation            0.000000e+00
## 4283                ribosome biogenesis            2.296954e-10
## 4279 ribosomal large subunit biogenesis            1.495557e-08
## 4278   ribosomal large subunit assembly            5.803312e-07
## 4281 ribosomal small subunit biogenesis            2.788234e-06
## 4282                  ribosome assembly            2.822479e-06
##      under_represented_pvalue numDEInCat numInCat          FDR
## 630                         1         19       23 0.000000e+00
## 4283                        1          8       13 5.420811e-07
## 4279                        1          5        5 2.353010e-05
## 4278                        1          4        4 6.847909e-04
## 4281                        1          4        5 2.220350e-03
## 4282                        1          4        5 2.220350e-03
## 
## [1] "set_38"
##  [1] "ICA1"          "OPHN1"         "CASS4"         "GPATCH2"      
##  [5] "CD69"          "IL1A"          "RCAN3"         "ZRANB3"       
##  [9] "IL1B"          "NRGN"          "TSPAN7"        "CACNA1D"      
## [13] "PLXDC1"        "CCDC171"       "MACROD2"       "KCNIP1"       
## [17] "CACNB4"        "COL25A1"       "LIPE-AS1"      "STX18-AS1"    
## [21] "MIR100HG"      "RP11-160E2.6"  "RP11-413N10.3" "ADAM22"       
## [25] "NCS1"          "NCOA7"         "CLVS2"         "CACNA1C"      
## [29] "MAPK13"        "DLGAP1"        "KCND3"         "DPP10"        
## [33] "CSMD1"         "KCND2"         "ANKS1B"        "PRKG1"        
## [37] "KCNIP4"        "MAGI2"         "KAZN"          "RYR2"         
## $reactome
##               category over_represented_pvalue under_represented_pvalue
## 113 cardiac conduction            1.656815e-06                0.9999999
## 599 muscle contraction            6.418779e-06                0.9999997
##     numDEInCat numInCat         FDR
## 113          6       18 0.001958355
## 599          6       24 0.003793499
## 
## $go_bp
##                                                  category
## 3683 regulation of monoatomic ion transmembrane transport
## 22                                       action potential
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3683            1.055834e-05                0.9999989          9       64
## 22              1.401989e-05                0.9999993          6       24
##             FDR
## 3683 0.03308693
## 22   0.03308693
saveRDS(goseq_res, sprintf("output/gene_set_enrichments_%s.RDS", 
                           file_tag))

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8955046 478.3   16112782 860.6         NA 16112782 860.6
## Vcells 16667435 127.2   31295163 238.8      65536 31295163 238.8
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] goseq_1.50.0           geneLenDataBase_1.34.0 BiasedUrn_2.0.10      
##  [4] fgsea_1.24.0           biomaRt_2.54.1         limma_3.54.2          
##  [7] tidyr_1.3.0            ggpubr_0.6.0           ggplot2_3.4.2         
## [10] data.table_1.14.8     
## 
## loaded via a namespace (and not attached):
##   [1] nlme_3.1-162                matrixStats_1.0.0          
##   [3] bitops_1.0-7                bit64_4.0.5                
##   [5] filelock_1.0.2              progress_1.2.2             
##   [7] httr_1.4.6                  GenomeInfoDb_1.34.9        
##   [9] tools_4.2.3                 backports_1.4.1            
##  [11] bslib_0.4.2                 utf8_1.2.3                 
##  [13] R6_2.5.1                    mgcv_1.8-42                
##  [15] DBI_1.1.3                   BiocGenerics_0.44.0        
##  [17] colorspace_2.1-0            withr_2.5.0                
##  [19] tidyselect_1.2.0            prettyunits_1.1.1          
##  [21] bit_4.0.5                   curl_5.0.1                 
##  [23] compiler_4.2.3              cli_3.6.1                  
##  [25] Biobase_2.58.0              xml2_1.3.4                 
##  [27] DelayedArray_0.24.0         rtracklayer_1.58.0         
##  [29] sass_0.4.5                  scales_1.2.1               
##  [31] rappdirs_0.3.3              Rsamtools_2.14.0           
##  [33] stringr_1.5.0               digest_0.6.31              
##  [35] rmarkdown_2.21              XVector_0.38.0             
##  [37] pkgconfig_2.0.3             htmltools_0.5.5            
##  [39] MatrixGenerics_1.10.0       dbplyr_2.3.2               
##  [41] fastmap_1.1.1               rlang_1.1.0                
##  [43] rstudioapi_0.14             RSQLite_2.3.1              
##  [45] BiocIO_1.8.0                jquerylib_0.1.4            
##  [47] generics_0.1.3              jsonlite_1.8.4             
##  [49] BiocParallel_1.32.6         dplyr_1.1.2                
##  [51] car_3.1-2                   RCurl_1.98-1.12            
##  [53] magrittr_2.0.3              GO.db_3.16.0               
##  [55] GenomeInfoDbData_1.2.9      Matrix_1.6-4               
##  [57] Rcpp_1.0.10                 munsell_0.5.0              
##  [59] S4Vectors_0.36.2            fansi_1.0.4                
##  [61] abind_1.4-5                 lifecycle_1.0.3            
##  [63] stringi_1.7.12              yaml_2.3.7                 
##  [65] carData_3.0-5               SummarizedExperiment_1.28.0
##  [67] zlibbioc_1.44.0             org.Hs.eg.db_3.16.0        
##  [69] BiocFileCache_2.6.1         grid_4.2.3                 
##  [71] blob_1.2.4                  parallel_4.2.3             
##  [73] crayon_1.5.2                lattice_0.20-45            
##  [75] splines_4.2.3               Biostrings_2.66.0          
##  [77] cowplot_1.1.1               GenomicFeatures_1.50.4     
##  [79] hms_1.1.3                   KEGGREST_1.38.0            
##  [81] knitr_1.44                  pillar_1.9.0               
##  [83] GenomicRanges_1.50.2        rjson_0.2.21               
##  [85] ggsignif_0.6.4              codetools_0.2-19           
##  [87] stats4_4.2.3                fastmatch_1.1-3            
##  [89] XML_3.99-0.14               glue_1.6.2                 
##  [91] evaluate_0.20               png_0.1-8                  
##  [93] vctrs_0.6.2                 gtable_0.3.3               
##  [95] purrr_1.0.1                 cachem_1.0.7               
##  [97] xfun_0.39                   broom_1.0.4                
##  [99] restfulr_0.0.15             rstatix_0.7.2              
## [101] tibble_3.2.1                GenomicAlignments_1.34.1   
## [103] AnnotationDbi_1.60.2        memoise_2.0.1              
## [105] IRanges_2.32.0